Data from: Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation
Creators
- Van Poucke, Kris1
- Haegeman, Annelies1
- Goedefroit, Thomas1
- Focquet, Fran2
- Leus, Leen1
- Horta Jung, Marília3
- Junker, Corina4
- Redondo, Miguel5
- Husson, Claude6
- Kostov, Kaloyan7
- Lyubenova, Aneta7
- Christova, Petya7
- Chandelier, Anne8
- Slavov, Slavcho7
- de Cock, Arthur9
- Bonants, Peter10
- Werres, Sabine4
- Palau, Jonàs11
- Marçais, Benoit12
- Jung, Thomas3
- Stenlid, Jan5
- Ruttink, Tom1
- Heungens, Kurt1
- 1. Instituut voor Landbouw en Visserijonderzoek
- 2. National Research Institute for Agriculture, Food and Environment
- 3. Phytophthora Research Centre*
- 4. Julius Kühn-Institut
- 5. Swedish University of Agricultural Sciences
- 6. Ministère de l'agriculture et de l'alimentation, Direction générale de l'alimentation*
- 7. Agrobioinstitute
- 8. Walloon Agricultural Research Centre
- 9. Westerdijk Fungal Biodiversity Institute
- 10. Wageningen University & Research
- 11. University of Lleida
- 12. Institut National de la Recherche Agronomique
Description
The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.
Notes
Funding provided by: Belgian Federal Science Policy Office
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002749
Award Number: BR/132/A1/RESIPATH-BE
Funding provided by: Fundação para a Ciência e a Tecnologia
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871
Award Number: BIODIVERSA/0002/2012
Files
locdata.txt
Additional details
Related works
- Is cited by
- 10.1186/s43008-021-00068-w (DOI)